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Rahayu AF, Hayashi A, Yoshimura Y, Nakagawa R, Arita K, Nakayama JI. Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly. J Biochem 2023; 174:371-382. [PMID: 37400983 DOI: 10.1093/jb/mvad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein that plays a critical role in heterochromatin assembly. HP1 proteins share a basic structure consisting of an N-terminal chromodomain (CD) and a C-terminal chromoshadow domain (CSD) linked by a disordered hinge region. The CD recognizes histone H3 lysine 9 methylation, a hallmark of heterochromatin, while the CSD forms a dimer to recruit other chromosomal proteins. HP1 proteins have been shown to bind DNA or RNA primarily through the hinge region. However, how DNA or RNA binding contributes to their function remains elusive. Here, we focus on Chp2, one of the two HP1 proteins in fission yeast, and investigate how Chp2's DNA-binding ability contributes to its function. Similar to other HP1 proteins, the Chp2 hinge exhibits clear DNA-binding activity. Interestingly, the Chp2 CSD also shows robust DNA-binding activity. Mutational analysis revealed that basic residues in the Chp2 hinge and at the N-terminus of the CSD are essential for DNA binding, and the combined amino acid substitutions of these residues alter Chp2 stability, impair Chp2 heterochromatin localization and lead to a silencing defect. These results demonstrate that the cooperative DNA-binding activities of Chp2 play an important role in heterochromatin assembly in fission yeast.
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Affiliation(s)
- Anisa Fitri Rahayu
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Aki Hayashi
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Kanagawa 230-0045, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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3
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Nakamura R, Nakayama JI. Multiple interfaces to recognize nucleosomal targets. J Biochem 2021; 171:257-259. [PMID: 34967395 DOI: 10.1093/jb/mvab139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/14/2022] Open
Abstract
In eukaryotic cells, DNA is tightly compacted as chromatin. Chromatin states must be dynamically changed to increase the accessibility of transcription factors to chromatin or to stably silence genes by higher-order chromatin structures known as heterochromatin. The regulation of chromatin needs cooperative action performed by a variety of proteins. Specific binding of transcription factors to target DNA is the initial step of chromatin regulation, and promotes changes in the post-translational modifications of histone tails, which themselves are recognized by a set of histone reader proteins. Recent biochemical studies have revealed that some transcription factors that recognize specific DNA sequences can also interact with histones. Furthermore, histone reader proteins that recognize specific histone tail modifications have been shown to have the ability to directly bind to DNA. In this commentary, we introduce recent advances in the elucidation of how chromatin regulating factors recognize nucleosomal targets.
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Affiliation(s)
- Rinko Nakamura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
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Abstract
Biomolecular condensates are membrane-less compartments that are formed through an assembly of proteins and nucleic acids in the cell. Dysregulation of biological condensates has been implicated in diseases such as neurodegeneration and cancer. Ribonucleic acid (RNA) is known to affect the assembly of proteins in vitro, if and how RNA is involved in regulating biomolecular condensates in cells is not well investigated. Here we examined two nuclear proteins, FUS and HP1α, in which RNA was found to have an opposite contribution for the assembly of these proteins. Reduction of nuclear RNA, by inhibiting the transcription, triggered assembly of FUS that had been distributed in the nucleoplasm, whereas it dispersed spontaneously formed HP1α assembly. Notably, the cell cycle-dependent phosphorylation-mimicking substitutions in HP1α promoted its assembly formation. These transcription inhibitor experiments are versatile to examine diverse roles of nuclear RNA in regulating biomolecular condensates, in both physiological and pathological conditions.
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Affiliation(s)
- Saho Matsui
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
| | - Ryu-Suke Nozawa
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
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Kamo N, Kujirai T, Kurumizaka H, Murakami H, Hayashi G, Okamoto A. Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors. Chem Sci 2021; 12:5926-5937. [PMID: 35342540 PMCID: PMC8872386 DOI: 10.1039/d1sc00731a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/21/2021] [Indexed: 12/21/2022] Open
Abstract
The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids.
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Affiliation(s)
- Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo Bunkyo-ku Tokyo 113-0032 Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo Bunkyo-ku Tokyo 113-0032 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Research Center for Advanced Science and Technology, The University of Tokyo Meguro-ku Tokyo 153-8904 Japan
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6
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Oki M, Masai H. Regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle. J Biochem 2021; 169:629-632. [PMID: 33772590 DOI: 10.1093/jb/mvab040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 11/12/2022] Open
Abstract
HP1 (Heterochromatin Protein 1), a key factor for the formation of heterochromatin, binds to the methylated lysine 9 of histone H3 (H3K9me), and represses transcription. While the H3K9me mark and HP1 binding are thought to be faithfully propagated to daughter cells, the heterochromatin structure could be dynamically regulated during cell cycle. As evidenced by the well-known phenomenon called Position Effect Variegation (PEV), heterochromatin structure is dynamically and stochastically altered during developmental processes, and thus the expression of genes within or in the vicinity of heterochromatin could be affected by mutations in factors regulating DNA replication as well as by other epigenetic factors. Recent reports show that HP1 also plays an important role in the maintenance and transmission of chromosomes. Like many other factors ensuring faithful chromosome segregation, HP1 family proteins are subjected to posttranslational modifications, most notably phosphorylation, in a cell-cycle dependent manner. Recent studies identified a conserved phosphorylation site that profoundly affects the functions of HP1 during mitotic phase. In this commentary, we discuss dynamic regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle.
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Affiliation(s)
- Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, JAPAN
| | - Hisao Masai
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, JAPAN, Tel: 81-3-5316-3220
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Pokorná P, Krepl M, Šponer J. Residues flanking the ARK me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2020; 1865:129771. [PMID: 33153976 DOI: 10.1016/j.bbagen.2020.129771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The chromodomain (CD) of HP1 proteins is an established H3K9me3 reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKme3S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. METHODS We acquired ~350 μs of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. RESULTS The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K0me3 and A-2 target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q-4 residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATKme3A motif, for which no structure is available, is predicted. CONCLUSIONS The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. GENERAL SIGNIFICANCE Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
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How HP1 Post-Translational Modifications Regulate Heterochromatin Formation and Maintenance. Cells 2020; 9:cells9061460. [PMID: 32545538 PMCID: PMC7349378 DOI: 10.3390/cells9061460] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) is a highly conserved protein that has been used as a classic marker for heterochromatin. HP1 binds to di- and tri-methylated histone H3K9 and regulates heterochromatin formation, functions and structure. Besides the well-established phosphorylation of histone H3 Ser10 that has been shown to modulate HP1 binding to chromatin, several studies have recently highlighted the importance of HP1 post-translational modifications and additional epigenetic features for the modulation of HP1-chromatin binding ability and heterochromatin formation. In this review, we summarize the recent literature of HP1 post-translational modifications that have contributed to understand how heterochromatin is formed, regulated and maintained.
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Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
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Williams MM, Mathison AJ, Christensen T, Greipp PT, Knutson DL, Klee EW, Zimmermann MT, Iovanna J, Lomberk GA, Urrutia RA. Aurora kinase B-phosphorylated HP1α functions in chromosomal instability. Cell Cycle 2019; 18:1407-1421. [PMID: 31130069 PMCID: PMC6592258 DOI: 10.1080/15384101.2019.1618126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/17/2019] [Accepted: 05/08/2019] [Indexed: 01/25/2023] Open
Abstract
Heterochromatin Protein 1 α (HP1α) associates with members of the chromosome passenger complex (CPC) during mitosis, at centromeres where it is required for full Aurora Kinase B (AURKB) activity. Conversely, recent reports have identified AURKB as the major kinase responsible for phosphorylation of HP1α at Serine 92 (S92) during mitosis. Thus, the current study was designed to better understand the functional role of this posttranslationally modified form of HP1α. We find that S92-phosphorylated HP1α is generated in cells at early prophase, localizes to centromeres, and associates with regulators of chromosome stability, such as Inner Centromere Protein, INCENP. In mouse embryonic fibroblasts, HP1α knockout alone or reconstituted with a non-phosphorylatable (S92A) HP1α mutant results in mitotic chromosomal instability characterized by the formation of anaphase/telophase chromatin bridges and micronuclei. These effects are rescued by exogenous expression of wild type HP1α or a phosphomimetic (S92D) variant. Thus, the results from the current study extend our knowledge of the role of HP1α in chromosomal stability during mitosis.
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Affiliation(s)
- Monique M. Williams
- Departments of Biochemistry and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Angela J. Mathison
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Trent Christensen
- Departments of Biochemistry and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Patricia T. Greipp
- Medical Genome Facility, Cytogenetics Core Laboratory, Rochester, MN, USA
| | - Darlene L. Knutson
- Medical Genome Facility, Cytogenetics Core Laboratory, Rochester, MN, USA
| | - Eric W. Klee
- Departments of Biochemistry and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Gwen A. Lomberk
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A. Urrutia
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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